Tue Oct 11 08:05:31 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:05:31 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5478524 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 9.324000 73.63100 ymin,ymax (A): -1.182000 63.79900 zmin,zma (A): -9.783999 37.49300 x,y,z range (A): 64.30700 64.98100 47.27700 scale (grids/A): 0.5478524 object centre (A): 41.47750 31.30850 13.85450 number of atom coordinates read : 3060 total number of charged atoms : 2914 net assigned charge : 11.50002 assigned positive charge : 459.2199 centred at (gu) : 90.22320 90.59975 90.19518 assigned negative charge : -447.7211 centred at (gu) : 90.32201 90.63042 90.15185 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6147 nv = 96 ne = 84 npr = 57295 no. pairs analyzed = 57295 no. exposed pairs = 4410 no. arc points = 31976 no. surface atoms = 1475 nbur = 1585 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 231 mr = 2772 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3283 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8009 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4037743E-10 1.1355213E-09 midg,1,midg; midg,igrid,midg 8.5911989E-10 6.3634098E-10 1,midg,midg; igrid,midg,midg 1.3958725E-09 5.6269378E-11 gauss-seidel spectral radius is 0.9828461 estimated iterations to convergence 63 setup time was (sec) 0.4100000 now iterating at: 08:05:31 rms-change max change #iterations 7.4868597E-02 13.47239 at 10iterations 4.9515222E-03 0.7942543 at 20iterations 3.3900456E-04 5.9996605E-02 at 30iterations 2.3899782E-05 3.6659241E-03 at 40iterations 2.1869018E-06 3.1089783E-04 at 50iterations finished qdiffx linear iterations at : 08:05:34 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.1869018E-06 3.1089783E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 08:05:35 3.366u 0.174s 0:04.14 85.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:05:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.643557 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 9.324000 73.63100 ymin,ymax (A): -1.182000 63.79900 zmin,zma (A): -9.783999 37.49300 x,y,z range (A): 64.30700 64.98100 47.27700 scale (grids/A): 1.643557 object centre (A): 41.47750 31.30850 13.85450 number of atom coordinates read : 3060 total number of charged atoms : 2914 net assigned charge : 11.50002 assigned positive charge : 459.2199 centred at (gu) : 90.66888 91.79816 90.58482 assigned negative charge : -447.7211 centred at (gu) : 90.96581 91.89108 90.45529 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 67067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31976 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19743 mr = 41738 m= 2045 mr = 12682 m= 60 mr = 934 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.3400000 number of dielectric boundary points 33561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 372 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 22342 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5478524 object centre at (A) : 41.47750 31.30850 13.85450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8260446E-03 8.7492820E-03 midg,1,midg; midg,igrid,midg -6.3568647E-03 -1.0851847E-02 1,midg,midg; igrid,midg,midg 3.1206999E-02 1.0487980E-02 gauss-seidel spectral radius is 0.9982379 estimated iterations to convergence 189 setup time was (sec) 0.5600000 now iterating at: 08:05:36 rms-change max change #iterations 3.394614 170.9689 at 10iterations 1.422488 58.25652 at 20iterations 0.5983808 21.83348 at 30iterations 0.2513822 8.860643 at 40iterations 0.1058992 3.694847 at 50iterations 4.4352222E-02 1.558867 at 60iterations 1.8723296E-02 0.7523608 at 70iterations 7.8948103E-03 0.2868843 at 80iterations 3.3285343E-03 0.1166527 at 90iterations 1.3955655E-03 5.9020996E-02 at 100iterations 5.8934768E-04 2.1436691E-02 at 110iterations 2.4847797E-04 9.3135834E-03 at 120iterations finished qdiffx linear iterations at : 08:05:43 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.4847797E-04 9.3135834E-03 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 08:05:44 7.769u 0.205s 0:08.82 90.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:05:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.465336 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 9.324000 73.63100 ymin,ymax (A): -1.182000 63.79900 zmin,zma (A): -9.783999 37.49300 x,y,z range (A): 64.30700 64.98100 47.27700 scale (grids/A): 2.465336 object centre (A): 41.47750 31.30850 13.85450 number of atom coordinates read : 3060 total number of charged atoms : 2914 net assigned charge : 11.50002 assigned positive charge : 459.2199 centred at (gu) : 91.00270 92.69724 90.87679 assigned negative charge : -447.7211 centred at (gu) : 91.44870 92.83648 90.68262 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 155650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31976 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67218 mr = 102961 m= 18889 mr = 50682 m= 3010 mr = 13641 m= 224 mr = 1879 m= 7 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 334 time to turn everything in is 0.8100000 number of dielectric boundary points 75743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 23283 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.643557 object centre at (A) : 41.47750 31.30850 13.85450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1560965 0.1098615 midg,1,midg; midg,igrid,midg -0.1157850 -7.1688883E-02 1,midg,midg; igrid,midg,midg 0.4392368 0.1544993 gauss-seidel spectral radius is 0.9991652 estimated iterations to convergence 273 setup time was (sec) 1.040000 now iterating at: 08:05:45 rms-change max change #iterations 8.938174 296.4393 at 10iterations 5.124311 131.2858 at 20iterations 2.912655 66.44292 at 30iterations 1.645007 37.28165 at 40iterations 0.9243019 20.64597 at 50iterations 0.5172191 11.22429 at 60iterations 0.2895193 6.422112 at 70iterations 0.1614654 4.172268 at 80iterations 8.9843564E-02 1.804426 at 90iterations 4.9947005E-02 1.038918 at 100iterations 2.7734429E-02 0.5981846 at 110iterations 1.5391301E-02 0.3166580 at 120iterations 8.5593434E-03 0.1780701 at 130iterations 4.7428915E-03 9.7557068E-02 at 140iterations 2.6279045E-03 5.3836823E-02 at 150iterations 1.4570185E-03 3.0877113E-02 at 160iterations 8.0997136E-04 1.6597748E-02 at 170iterations 4.4802710E-04 8.9406967E-03 at 180iterations finished qdiffx linear iterations at : 08:05:56 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 4.4802710E-04 8.9406967E-03 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 08:05:56 12.361u 0.199s 0:12.86 97.5% 0+0k 0+0io 0pf+0w